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SEA Complex

Modeling of the SEA complex PubMed logo

crossWarning: these files have not yet been verified to work with the latest version of IMP. We will update this page when they have been. The files are also available at GitHub.
Additional software needed to use these files: IMP install instructions

Anaconda logo To install the software needed to reproduce this system with the Anaconda Python command line tool (conda), run the following commands:

conda config --add channels salilab
conda install imp

UCSF logo To set up the environment on the UCSF QB3 cluster to run this system, run:

module load imp
Tags affinity purification chemical crosslinks MODELLER PMI

These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the SEA complex using 188 DSS chemical cross-links and 23 composites from affinity purification.

First, MODELLER is used to generate initial structures for the individual components where reliable templates are available. Then, IMP / PMI are used to model these components using the DSS crosslinks and the affinity purification data for the entire SEA complex.

The scripts work with the 65734ec version (develop branch) of IMP and the 47dafcc version (develop branch) of PMI.

A full description of the scripts can be found in Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway.

List of files and directories:

Running the MODELLER scripts:

Running the IMP/PMI scripts for the SEA complex:

To produce a single model with 1:3 stoichiometry and rotational symmetry, as in the publication, use the run_qsub.sh script:

run_qsub.sh 50000 20000 3 True

For the publication, this script was run 885 times to generate the final ensemble, which was then clustered to produce the 340 models in the output directory.

This script in turn runs scripts/sj_SEA_multi_layers.py, which if desired can be run with different options to explore other representations and sampling options.

Information

Author(s): Seung Joong Kim, Riccardo Pellarin, and Peter Cimermancic

Date: October 6th, 2014

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Last known good IMP version: build info build info

Testable: Yes.

Parallelizeable: No

Publications: